Maharaj took 4-20 in the first ODI in Durban and then followed that up with figures of 2-54 at the Wanderers as the Proteas took an unassailable 2-0 in the lead in teh three-match series.
The 36-year-old left-arm spinner moved up three places to sit behind Pakistan slow-bowler Abrar Ahmed while the top-ranked bowler in the 50-over format is Afghanistan's Rashid Khan.
Proteas to gain in the ICC ODI batting rankings are Matthew Breetzke, who scored a century in Durban that lifted him 19 places to 21st. while David Miller returns to the rankings in 41st position after scoring a hundred in Johannesburg.
Proteas captain Temba Bavuma, who also notched a ton in the second match at the Wanderers, has advanced 10 slots to 32nd position, while Marco Jansen (up 42 places to 87th) has also progressed.
India batting icon Virat Kohli has closed the gap on captain Shubman Gill at the top of the batting rankings, despite both players scoring centuries in the first ODI against the West Indies in Thiruvananthapuram on Sunday.
Aiden Markram says it was "nice having a little bit of time off" but is ready to contribute as the Proteas eye an ODI series victory against Australia at the Wanderers on Sunday.
David Miller produced a career-best innings and Temba Bavuma added a century while the spinners dominated for the Proteas as they secured a second consecutive victory over Australia, winning the second ODI by 32 runs at the Wanderers in Johannesburg.
Anrich Nortje has been selected in an expanded 18-man Proteas Test squad for the series against Australia despite having not played a red-ball game in three years, while Kagiso Rabada is also included.
South Africa recovered from a difficult start to defeat Australia by 67 runs in the first ODI in Durban, taking an early lead in the three-match series.
